Eureka! Easy Genotyping for Tough Samples

The why of Juno

“That’s too much DNA,” a pharmaceutical company researcher commented to Fluidigm Senior Product Manager Nico Tuason last June. “I can't possibly get that much DNA or that high of a concentration for all of our study samples—not with the purification kit I'm using now.”

Next-generation sequencing (NGS), STR and SNP genotyping and microarrays require a lot of pure, PCR inhibitor-free DNA, sometimes at microgram levels. These methods demand high-quality, high-concentration DNA to prevent false data caused by allelic dropouts. There’s no shortage of scientists recounting tales of sample collection woes.

“While it’s notoriously challenging to gather sufficient amounts of usable DNA,” Tuason noted, “it remains the essential raw material for pharma and ag-genomics study and for translational or clinical research.”

Purification is a common way to obtain clean DNA yet it’s a tedious, costly process that can yield variable concentrations. When there’s a shortage of DNA, scientists have two choices: they can extract and purify again, which adds even more to the time, price and potential for error, or they can re-collect, which isn’t always possible when dealing with FFPE (formalin-fixed, paraffin-embedded) or noninvasively collected samples. Sometimes the source of the sample is gone. Both choices also raise the risk of sampling errors.

With human samples, the person must return for another blood draw or send in another swab or saliva sample—opening the door for noncompliance. With plants and animals, there’s another level of complexity since sample sources such as salmon and wolves move about and migrate. Chipping more from a seed or picking extra leaves from a seedling may make them unviable. Banked FFPE samples can run out (or degrade over time). There may be no second chance to gather samples.

The risk of such complications forces researchers to cobble together workarounds in their lab’s standard operating procedures. This means collecting duplicates or splitting samples, which cost more in both labor and financial outlay.

Juno genotyping

The Juno system from Fluidigm is engineered to genotype meager DNA samples without need for workarounds. This is especially germane to noninvasive sample collection, which inherently poses more of a challenge. “Even after purification, PCR inhibitors can remain or the DNA can have insufficient concentration,” Tuason pointed out. “The Juno IFC (integrated fluidic circuit) empowers researchers to start from small amounts of compromised material.” Where a typical purification kit might yield 25 ng/µL, Juno can genotype from a mere 10 percent of that amount so workarounds, re-extractions and re-collections are unnecessary.

Juno's power to genotype from low-concentration DNA is a major milestone because even if fortune favors your work with adequate purified DNA material, other factors can impact samples after purification, quantification, normalization and genotyping.

Now imagine having the freedom to collect compliant samples noninvasively, even in sensitive environments, from fallen leaves, fruit or bark; animal droppings; or hair or skin—samples that typically yield unsatisfactory DNA for genomic research. Envision starting from low-concentration samples without having to capture or sacrifice test subjects. Picture needing less DNA; think of the doors that will open with the ability to test samples degraded from storage.

Juno makes this possible by enriching for target DNA and diluting out unwanted contaminants from the original sample matrix and extraction. Enrichment involves preamplifying target DNA primers specific to the locus. Juno preamplifies and genotypes in a single, hands-off protocol. The only manual preparation required is independently transferring the DNA sample and assay mixes into the appropriate IFC inlets. The automated Juno workflow takes care of the rest.

The IFC is ready to read on the Biomark HD in less than three hours. With Juno, labs can run hundreds of samples in a single day and still have time for other experiments. With whole workdays no longer consumed by this routine method, researchers are free to do more science.

“Juno means labs can do all that now, with streamlined simplicity and speed,” Tuason added. “This is a really big deal for genomics researchers.”